Discoveries in genetics science are very important to
evolution theory. For example, genetics has provided substantial confirmation
of the species descendency concept. Genetic fingerprinting can not only
determine if a person is related to another person but also the extent of the
relationship. In the same manner, it is possible to determine that all Earth
species are related, determine how closely they are related, and even
approximate when two species diverged from each other. Mice and humans shared
common ancestors approximately 30 million years ago.

To review, traditional mechanics theory says that the
evolution process is entirely driven by differences in expressed
phenotypic design between organisms that are then selected or rejected by
natural selection. Phenotypic design includes physical properties and
inherited behaviors that plausibly affect the probability that the organism
will survive longer and reproduce more. Expressed means that the design
property has to be operative during the life of the organism such that its
existence affects survival or reproduction. Latent properties cannot affect
evolution according to traditional theory. Evolution is essentially
performance driven: Does the mutant design change allow the organism to
survive longer and breed more?

ISSUE: Evolution of Inheritance Systems

One issue with traditional theory concerns the
inheritance systems that handle transmission of genetic design information
between generations of an organism. The designs of these systems nominally do not affect the
phenotypic design and therefore performance (survival and reproduction) of an
organism except in a negative way. An asexually reproducing organism could
have the same or better phenotypic design as a sexually reproducing organism
from a performance viewpoint. And yet sexually reproducing organisms developed
from asexually reproducing organisms and this involved the evolution of very
substantial additional complexity in their inheritance systems including
paired chromosomes, meiosis, etc. Since sexual reproduction is performance
neutral or disadvantageous, what drove the evolution of the inheritance
system? Alternative evolutionary mechanics theories (especially evolvability)
speak to this issue.

ISSUE: Digital Genetics

Genetics discoveries have determined that genetic
information is digital in nature. Organism design information is carried by the
sequence in which base molecules are strung together to produce a DNA
molecule. Because genetic information is digital, inheritance systems share
properties with and must follow the same rules as any other digital
information transmission or storage system. Genetics discoveries show that this is indeed the case and
that genetic data has a complex digital data structure including formats, “words”,
language, codons, synchronization features, etc. Many complex genotypic design features of this system
appear to have no phenotypic design consequence and therefore no traditional
evolutionary motivation for their development although they do have
evolutionary effects as described below. What drove evolution of the genome?

The decoding of the human genome has revealed that the
genome consists of 3.3 billion genetic code letters equivalent to 825
megabytes of data. Much of this is extremely repetitive and therefore contains
little information. Only about 5 percent (41 megabytes) is thought to have
phenotypic (design) consequence. There are therefore finite limits to the
number of design parameters that can be specified by the genetic code as well
as limits on the precision with which those parameters can be specified. See
Digital Genetics.

ISSUE: Evolutionary Sub-processes

The traditional concept is that the evolution process
happens in two steps:

A mutation occurs in a single individual that changes
the inheritable expressed phenotypic design of the organism.

Natural selection selects those changes that improve
organism performance incorporating them into the species genotype.

Once a beneficial mutation occurs, the individual organisms
possessing the mutant genotype immediately survive longer and perform better
in propagating their mutant design. This is sometimes referred to as the “one
mutation at a time concept.” Darwin suggested that any single mutational
change would need to have only a minor phenotypic effect in order to propagate
because a large change would almost certainly be adverse. The traditional view
emphasizes the evolutionary importance of individual organisms as
opposed to groups or populations and also suggests that, once a beneficial
mutation occurred, propagation of that change could be rapid.

Genetics discoveries show that although mutations and
natural selection are very central to the evolution process, there are many
intermediate steps also involved in the evolution of complex, sexually
reproducing organisms. The steps involved might look more like:

Remaining mutations propagate in a population. Any two
individuals may have a large number of genetic differences. The same
individual could possess many genetic differences between its two genomes.

Genetic data can be occasionally copied producing a
duplicate of some amount of genetic data.

Some mutations have no phenotypic effect but encourage
subsequent mutations that move (transpose) data from one location in the
data format (genome) to another location.

Some mutations have no phenotypic effect but can
encourage subsequent copying and duplication.

Copied data can introduce redundancy and/or create a
data basis for new genetic instructions. Redundancy can increase
robustness or the tendency to resist alteration of the controlled
function by subsequent mutation.

Recombination in miosis can produce individuals having
different combinations of genetic differences and therefore different
phenotypic designs even though they are descendents of the same parents.
Because of cascading, phenotypic differences resulting from recombination
can be much larger than differences resulting from an individual
propagatable mutation.

Inheritance is affected by the relative location (locus)
of mutational differences in the genetic data structure (genome) due to the
genetic linkage principle(1) – encourages group inheritance of linked
mutational differences. Transposing of data affects this by changing
relative location.

The above brief summary grossly understates the sort of
evolutionary process complexity that has emerged from study of inheritance
mechanisms. The sub-processes interact in very complex ways and tend to
operate on long time frames even compared to evolutionary time standards. This
affects the plausibility of group selection as described below. All of the
steps appear to have evolvability benefits. In mammals, it is thought that less
than five percent of genetic data has phenotypic effect (gene exons and
promoters) while much of the remaining “junk DNA” has plausible evolutionary
effects by guiding subsequent mutational changes.

Note that the complex concept is more powerful than the
traditional concept because it allows for the possibility that a particular
combination of mutational changes could result in a benefit even though each
individual change, considered by itself, was mildly adverse.

ISSUE: Genes

Genes specify organism phenotypic design and are a
specific data structure within the overall genomic data structure mentioned
above. The evolution of progressively more complex organisms has required the
evolution of progressively more genes. The evolution of a new gene having a
different function is, for many reasons, a particularly difficult step in the
evolution process. Indeed, genetics discoveries show that similar related
organisms (e.g. mammals) have virtually the same genes. Their phenotypic
differences are the result of relatively minor differences within the genes.
Therefore: “Genes live longer than species” and represent a long-term process
even relative to species life times. This is the basis of the gene-oriented
alternative evolutionary mechanics theories.

ISSUE: Universality of Evolution Process

Darwin and traditional evolutionary mechanics theory
assumed that the evolution process is the same for all species. All species
presumably were subject to mutational change and also to natural selection.
However, genetics discoveries disclosed gross differences in inheritance
mechanisms that clearly affect propagation of mutational changes. Simple
organisms (e.g. bacteria) only possess one (haploid) set of genetic data while
most complex organisms possess two (diploid) sets of genetic data. In the latter
case, phenotypic design is determined by the combined effect of both sets of
genetic data. Further, early genetics discoveries revealed that in many cases
one state (allele) of a mutational difference dominated the design such that
the opposite allele would have essentially no phenotypic effect unless both
sets of genetic data contained the same recessive allele. Propagation of
mutational changes is therefore very different in diploid organisms because an
adverse mutational change that was recessive could propagate more readily than
in the haploid case while a beneficial but recessive mutational change would
propagate less well than in the haploid case. Further analysis disclosed many
other differences that plausibly affect propagation (e.g. X or Y linking,
mitochondrial DNA, etc.) Obvious questions result:

If the evolution process is different in different
organisms potentially enormous complexity results. Data acquired from study
of bacteria is not necessarily applicable to complex organisms, etc. Perhaps
mammals evolve in a different manner than plants? Are there many factors
that influence the evolution process? Which species possess them? To what
extent?

From a traditional mechanics standpoint, the diploid
inheritance mechanism appears to be a step backward. Propagation of
beneficial changes is inhibited while propagation of adverse changes is
encouraged. Why would a backward step evolve and be retained?

Everybody agrees that diploid genomes and sexual
reproduction are evolved designs. Is it possible that therefore organisms
can evolve differences in their evolutionary processes? Can they evolve
improvements in their evolutionary processes?

Traditional “one mutation at a time” evolutionary
mechanics theory assumes that each mutational change is individually selected
or rejected by the evolution process. A mutational change is the selectable
property. However we now know that the digital
nature of genetic data means that a genome either possesses or does not
possess a given mutational difference (generally a single nucleotide
polymorphism or SNP), a binary situation. Any organism
property that is more or less continuously variable in a population (think
bell-shaped curve) must result from combining many genetic differences that
simultaneously exist in that population and affect the given parameter. Further, virtually all potentially
complex selectable properties (e.g. strength, intelligence, speed, etc.) in complex
organisms result from combining many mutational differences in a
particular manner. The human population at large is now thought to
currently contain millions of individual genetic differences, each
presumably resulting from a different mutation in a different individual.

Therefore, in complex organisms, a selectable property is not the same
as a mutational difference. This sort of logic tends to deemphasize the
importance of individuals and individual possession of mutational changes
relative to the importance of particular combinations of mutational
changes where the underlying mutations are relatively widely dispersed in a
population. This in turn favors alternative evolution mechanics theories.

ISSUE: Evolutionary Rapidity and Individual vs. Group Selection

Everybody agrees that the design of anything is a
compromise. Theorists agree that a group benefit could be a compromise with
individual disadvantage. Functionally there is no difference between
individual survival and group survival. Either way, dead is dead, extinct is
extinct. Therefore those who disagree with the group selection concept do so
because of a timing issue. Wouldn’t an individual disadvantage tend to
act more rapidly than a group advantage? How would an individually
disadvantageous design survive long enough to populate a group?
Wouldn’t a group benefiting design need to be possessed by most members of a
group to be effective? Traditional theorists point to selective breeding in
suggesting that a design feature representing an individual disadvantage would
select out prior to the point in time at which a group benefit could be effective.
Selective breeding can indeed cause enormous phenotypic change in a very brief
time.

However, selective breeding (or rapid natural selection)
can only affect (select among) the relatively tiny portion (estimated at 0.1 percent in
humans) of genetic data that varies between members of a population,
essentially only the last step of the complex evolution process described
above. As a result, selective breeding for any one design parameter introduces
changes (nominally adverse) to other parameters. In most cases the breeder
does not care about the unintended changes but evolutionary advantage depends
on the combined net effect of all of the organism’s characteristics so
evolution is affected by the introduction of adverse changes. Change
resulting from selective
breeding is not the same as evolutionary change. Evolution, by means of new mutations
and utilizing all the sub-processes can achieve much more comprehensive
optimization of all of the organism’s characteristics. Because the
comprehensive process is much longer, the apparent timing difference between
group and individual selection is dramatically reduced increasing the feasibility
of group selection. This issue is probably the single most important issue in
the continuing controversy between traditional and alternative evolutionary
mechanics theories.

ISSUE: Unnatural Variation

Darwin and subsequent theorists agreed that variation in
inheritable organism design characteristics in a species population was
essential to the evolution process. Without variation, there would be nothing
for natural selection to select. Darwin and traditional theory assume that
variation is caused by mutations, that all species are susceptible to
mutations, and that therefore natural variation is a fundamental property of
life.

However, we now understand that “natural” variation in
complex organisms is actually largely the result of evolved design
characteristics including meiosis, recombination, and many others. Trivial
example: An inheritable behavior that caused an animal to prefer mating with
non-relatives would increase variation in its population. Without the evolved, variation
enhancing characteristics, variation in complex organisms would be much less,
possibly negligible.

The idea that a property that is essential to the
evolution process is
itself the result of evolved characteristics leads directly to the
evolvability alternative mechanics theory.

(1) Genetic linkage: Because of the
meiosis genetic crossover mechanism, the probability of inheriting specific
mutational alleles as a group from the same ancestor depends on the genomic
(data) distance between them. Distant alleles on the same chromosome or on
different chromosomes will be more randomly selected from the organism's two
parents. Alleles close together on the same chromosome will tend to be inherited
as a group.